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There aren't any hooks or controls within the Reports plugin to control what it reports. Currently, it collects and stores data for all blogs on a multisite install. Even those with the different privacy settings under /wp-admin/options-privacy.php
Any chance you can republish with a couple hooks to address the privacy options, OR to just make it filter results that aren't "public" as assigned by the "Sitewide Privacy Options for WordPress Multisite" plugin (which you also produce).